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- PDB-6v1p: Structure of VIM-2 bound to QPX7728 at 1.20 A -

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Basic information

Entry
Database: PDB / ID: 6v1p
TitleStructure of VIM-2 bound to QPX7728 at 1.20 A
ComponentsBeta-lactamase class B VIM-2
KeywordsHYDROLASE/HYDROLASE Inhibitor / carbapenemase / boronate / inhibitor / beta-lactamase / HYDROLASE / HYDROLASE-HYDROLASE Inhibitor complex
Function / homology
Function and homology information


antibiotic catabolic process / beta-lactamase / hydrolase activity / metal ion binding
Similarity search - Function
: / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
Similarity search - Domain/homology
ACETATE ION / Chem-QNA / Metallo-beta-lactamase type 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsPemberton, O.A. / Chen, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Health & Human Services (HHS)HHSO100201600026C United States
CitationJournal: J.Med.Chem. / Year: 2020
Title: Discovery of Cyclic Boronic Acid QPX7728, an Ultrabroad-Spectrum Inhibitor of Serine and Metallo-beta-lactamases.
Authors: Hecker, S.J. / Reddy, K.R. / Lomovskaya, O. / Griffith, D.C. / Rubio-Aparicio, D. / Nelson, K. / Tsivkovski, R. / Sun, D. / Sabet, M. / Tarazi, Z. / Parkinson, J. / Totrov, M. / Boyer, S.H. ...Authors: Hecker, S.J. / Reddy, K.R. / Lomovskaya, O. / Griffith, D.C. / Rubio-Aparicio, D. / Nelson, K. / Tsivkovski, R. / Sun, D. / Sabet, M. / Tarazi, Z. / Parkinson, J. / Totrov, M. / Boyer, S.H. / Glinka, T.W. / Pemberton, O.A. / Chen, Y. / Dudley, M.N.
History
DepositionNov 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-lactamase class B VIM-2
B: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,67816
Polymers51,3872
Non-polymers1,29114
Water10,629590
1
A: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3398
Polymers25,6931
Non-polymers6457
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactamase class B VIM-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3398
Polymers25,6931
Non-polymers6457
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.670, 79.120, 77.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11B-657-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-lactamase class B VIM-2 / BlaVIM-2 / Metallo beta-lactamase / Metallo-beta lactamase protein / Metallo-beta-lactamase VIM-2 / ...BlaVIM-2 / Metallo beta-lactamase / Metallo-beta lactamase protein / Metallo-beta-lactamase VIM-2 / VIM-2 / VIM-2 beta-lactamase / VIM-2 class B metallo b-lactamase / VIM-2 metallo beta-lactamase / VIM-2 type metallo-beta-lactamase


Mass: 25693.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: blaVIM-2, bla vim-2, bla-VIM-2, blasVIM-2, blaVIM2, VIM-2, vim-2
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9K2N0

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Non-polymers , 5 types, 604 molecules

#2: Chemical ChemComp-QNA / (1~{a}~{R},7~{b}~{S})-5-fluoranyl-2,2-bis(oxidanyl)-1~{a},7~{b}-dihydro-1~{H}-cyclopropa[c][1,2]benzoxaborinine-4-carboxylic acid


Mass: 238.985 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H9BFO5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 590 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.84 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.17 M Ammonium acetate, 0.085 M Sodium acetate pH 4.6, 25.5% (w/v) PEG4000, 15% (v/v) Glycerol, 1 mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→42.54 Å / Num. obs: 122856 / % possible obs: 96.5 % / Redundancy: 7.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.15 / Net I/σ(I): 9
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 5.3 % / Rmerge(I) obs: 2.019 / Num. measured all: 24912 / Num. unique obs: 4666 / CC1/2: 0.457 / Net I/σ(I) obs: 1.7 / % possible all: 75.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.4 Å35.2 Å
Translation4.4 Å35.2 Å

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
PHASER2.8.2phasing
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
iMOSFLM7.2.2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KO3

1ko3


Resolution: 1.2→35.2 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 16.88
RfactorNum. reflection% reflection
Rfree0.1682 11621 4.94 %
Rwork0.1426 --
obs0.1439 122692 95.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 58.44 Å2 / Biso mean: 17.7143 Å2 / Biso min: 5.84 Å2
Refinement stepCycle: final / Resolution: 1.2→35.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3498 0 68 590 4156
Biso mean--12.88 33.65 -
Num. residues----464
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.210.30992420.29275415565769
1.21-1.230.28042960.26935991628777
1.23-1.240.29053210.26486569689084
1.24-1.260.26543920.24887167755992
1.26-1.280.23653930.22157495788896
1.28-1.290.2483270.20597546787396
1.29-1.310.22143780.20267443782196
1.31-1.330.22993160.1927586790296
1.33-1.350.20573310.1787561789296
1.35-1.370.2153860.17147550793696
1.37-1.40.20473820.16287599798197
1.4-1.420.1933650.16887477784297
1.42-1.450.19414290.16247591802097
1.45-1.480.18723870.15147587797497
1.48-1.510.16394190.14017519793897
1.51-1.550.14384160.12757620803697
1.55-1.590.16314200.12537600802098
1.59-1.630.1414220.12247580800298
1.63-1.680.16213900.12027694808498
1.68-1.730.154280.11437620804898
1.73-1.790.14823940.11347687808198
1.79-1.860.13854100.11747675808599
1.86-1.950.16034180.127703812199
1.95-2.050.17354450.12117650809599
2.05-2.180.14414260.11747730815699
2.18-2.350.16114610.12457727818899
2.35-2.590.15394140.132277758189100
2.59-2.960.15814040.13977808184100
2.96-3.730.14053560.130978568212100
3.73-35.20.16754530.14717705815899

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